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(-) Description

Title :  EM FITTED MODEL OF BACTERIAL HOLO-TRANSLOCON
 
Authors :  C. Schaffitzel, M. Botte
Date :  20 Nov 16  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  14.00
Chains :  Asym./Biol. Unit :  C,D,E,F,G,Y
Keywords :  Holotranslocon, Membrane Protein Insertion Machinery, Chaperone, Protein Secretion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Botte, N. R. Zaccai, J. L. Nijeholt, R. Martin, K. Knoops, G. Papai, J. Zou, A. Deniaud, M. Karuppasamy, Q. Jiang, A. S. Roy, K. Schulten, P. Schultz, J. Rappsilber, G. Zaccai, I. Berger, I. Collinson, C. Schaffitzel
A Central Cavity Within The Holo-Translocon Suggests A Mechanism For Membrane Protein Insertion.
Sci Rep V. 6 38399 2016
PubMed-ID: 27924919  |  Reference-DOI: 10.1038/SREP38399

(-) Compounds

Molecule 1 - PROTEIN TRANSLOCASE SUBUNIT SECY
    Chains: Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECY, PRLA, B3300, JW3262
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - PROTEIN TRANSLOCASE SUBUNIT SECE
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECE, PRLG, B3981, JW3944
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 3 - PROTEIN-EXPORT MEMBRANE PROTEIN SECG
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECG, B3175, JW3142
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: P12,PREPROTEIN TRANSLOCASE BAND 1 SUBUNIT
 
Molecule 4 - PROTEIN TRANSLOCASE SUBUNIT SECD
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECD, B0408, JW0398
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 5 - PROTEIN TRANSLOCASE SUBUNIT SECF
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECF, B0409, JW0399
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 6 - MEMBRANE PROTEIN INSERTASE YIDC
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YIDC, B3705, JW3683
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FOLDASE YIDC,INNER MEMBRANE PROTEIN YIDC,MEMBRANE INTEGRASE YIDC,OXA1EC

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : CDEFGY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5MG3)

(-) Sites  (0, 0)

(no "Site" information available for 5MG3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MG3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val E:450 -Ala E:451

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MG3)

(-) Exons   (0, 0)

(no "Exon" information available for 5MG3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain C from PDB  Type:PROTEIN  Length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeee.....eeeeeeeeee.......eee.........eeeeeeee.....................eee......eeeeeeeee.....eeeeeeeee....eeeeeeeee......eeeeeeeeeeee..........eeeee......eeee............eee..eeeee...eeeee......eeeeeeee....eeeeeeee..eee....eeeeeeeeeeee.hhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhh......hhhhhhh...........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mg3 C  57 QGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLTFRGAAYSTPDAAYAAYAFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHFISQPLFKLLKWIHSFVGNWGFSIIIITFIVRGIMYPLTKAQYTSMAKMRMLQPKIQAMRERLGDDKQRISQEMMALYKAEKVNPLGGCFPLLIQMPIFLALYYMLMGSVELRQAPFALWIHDLSAQDPYYILPILMGVTMFFIQKMSPTTVTDPMQQKIMTFMPVIFTVFFLWFPSGLVLYYIVSNLVTIIQQQLIY 532
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206|      226       236       246       256       266       276       286       296       306       316      |337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527     
                                                                                                                                                                               206|                                                                                                       323|                                                                                                                                                                                                     
                                                                                                                                                                                217                                                                                                        335                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.........ee.....ee...........hhhhhh......ee...................hhhhhhh..........eee....eeeeeee.......eeeeeehhhhhhhhhhhhhhhh..eeeeeeee...............eeeeeeeeeee.......eeee........hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mg3 D   1 MLNRYPLWKYVMLIVVIVIGLLYALPNAVQQNINILRNRVNQLGVAEPVVQRQGADRIVVELPGIQDTARAKEILGATATLEFRLVNTNVDQAAAASGRVPGDSEVKQTREGQPVVLYKRVILTGDHITDSTSSQDEYNQPQVNISLDSAGGNIMSNFTKDNIGKPMATLFVEYKDSGKKDANGRAVLVKQEEVINIANIQSRLGNSFRITGINNPNEARQLSLLLRAGALIAPIQIVEERTIGPTLGMQNIEQGLEACLAGLLVSILFMIIFYKKFGLIATSALIANLILIVGIMSLLPGATLSMPGIAGIVLTLAVAVDANVLINERIKEELSNGRTVQQAIDEGYRGAFSSIFDANITTLIKVIILYAVGTGAIKGFAITTGIGVATSMFTAIVGTRAIVNLLYGGKRVKK 612
                                    10        20      |228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608    
                                                     27|                                                                                                                                                                                                                                                                                                                                                                                                  
                                                     226                                                                                                                                                                                                                                                                                                                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 5mg3 E 444 TKGKATVAFAREARTEVRKVIWPTRQETLHTTLIVAAVTAVMSLILWGLDGILVRLVSFITGLRF 508
                                   453       463       473       483       493       503     


Chain F from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeee....hhhhhhhhhhhhh......eeeee..eeeeee...........................eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mg3 F  14 RKVYDFMRWDYWAFGISGLLLIAAIVIMGVRGFNWGLDFTGGTVIEITLEKPAEIDVMRDALQKAGFEEPMLQNFGSSHDIMVRMPPAEGETGGQVLGSQVLKVINESTNQNAAVKRIEFVGPSVGADLAQTGAMALMAALLSILVYVGFRFEWRLAAGVVIALAHDVIITLGILSLFHIEIDLTIVASLMSVIGYSLNDSIVVSDRIRENFRKIRRGTPYEIFNVSLTQTLHRTLITSGTTLMVILMLYLFGGPVLEGFSLTMLIGVSIGTASSIYVASALALKLGMK 302
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293         


Chain G from PDB  Type:PROTEIN  Length:32
                                                                
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 5mg3 G 509 SSGSGNFMTRMTALLATLFFIISLVLGNINSN 540
                                   518       528       538  


Chain Y from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhh.....................hhhhhhhhh............hhhhhhhhhhhhh....hhhhhh.............hhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh...hhhhhhhhhhhhhhhhhh...................................hhhhhhh......hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mg3 Y   1 MAKQPGLDFQSAKGGLGELKRRLLFVIGALIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISASIIIQLLTVVHPTLAEIKKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISLYLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGYGR 443
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5MG3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MG3)

(-) Gene Ontology  (21, 76)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Val E:450 - Ala E:451   [ RasMol ]  
 

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  5mg3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SECE_ECOLI | P0AG96: 2akh 2aki 3j45 3j46 4v6m 5gae
        SECG_ECOLI | P0AG99: 2akh 2aki 3j45 3j46
        SECY_ECOLI | P0AGA2: 2akh 2aki 3j45 3j46 4v6m 5abb 5gae
        YIDC_ECOLI | P25714: 3blc 3bs6 4utq 5m5h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MG3)